Nucleic acids: DNA and RNA Done By Majed Felemban

1. Nucleic acids: DNA and RNADone ByMajed Felemban

2. DNA • Double helix • 2 chains • Building blocks • Nucleotides • DNA directs • Is own replication • Directs RNA synthesis → protein synthesis Campbell and Reece, P86

3. Complete human genome In Eukaryotes (animals, plants, fungi)

4. Main chromosome is one large, continuous loop Hundreds to thousands of genes May have smaller loops, with a few genes each May be swapped between bacteria Antibiotic resistance, etc. In Prokaryotes (bacteria, archaea)

5. Replication Transcription Translation

6. Roles of Nucleic Acids • DNA • Responsible for inheritance • Codes for proteins and functional RNAs • Genes • Regulatory sequences • Control which genes are transcribed, and when • Other unknown functions • 80-90% of the human genome has no known function Campbell and Reece, P86, 87

7. Roles of Nucleic Acids • RNA • Information transmission (mRNA) • Processing and transport (tRNA, rRNA, snRNA) • Catalytic (ribozymes) • Regulation and feedback (siRNA) • Unit of inheritance (retroviruses) • Other…? Campbell and Reece, P86, 87

8. NUCLEIC ACID STRUCTURES • Nucleic Acid chemistry is the same for all life on earth. • DNA & RNA are polymers of monomers - nucleotides. • Each nucleotide has three components X (Deoxy)ribonucleic Acid X 1. PHOSPHORIC ACID = STRUCTURAL 2. (DEOXY)RIBOSE SUGAR = STRUCTURAL 3. NITROGENOUS BASES = INFORMATIONAL Campbell and Reece, 86

9. Campbell and Reece, P87

10. Phosphoric Acid & Related Compounds D • Phosphoric acid is • Triprotic. • Reacts with CHO’s or alcohols to form esters.

11. - As found in DNA & RNA at pH7 Phosphoric Acid & Related Compounds • Phosphoric acid is • Triprotic. • Reacts with alcohols to form esters.

12. H The sugar may be Ribose (in RNA) or Deoxyribose (in DNA) Ribose Deoxyribose Phosphate can covalently bond to C3 and C5 Bases (A,C,G,T or U) can covalently bond to C1

13. (RNA) (DNA) Bases in DNA and RNA

14. A Base Joined To A Ribose Sugar Is Called A Nucleoside Purines bond N-9 to 1’ Carbon of sugar or H The carbons in the ribose are now designated as C prime (or C’) to distinguish them from those in the base. Pyrimidines bond at N-1 to C-1’ or H

15. When Phosphate is Bound to a Nucleoside it is Called a Nucleotide • ATP, GTP, CTP, UTP (NTPs) are substrates for RNA synthesis • dATP, dGTP, dCTP, dTTP (dNTPs) are substrates for DNA synthesis

16. Mononucleotides as they Occur in DNA & RNA A,C,G or T (DNA) or A,C,G or U (RNA) DNA All nucleotides are asymmetrical RNA

17. 5’C = 3’C = DNA & RNA are Polymers of Nucleotides Four Nucleotides With 5’ to 3’ Phosphodiester Linkages All DNA and RNA polymers are asymmetrical with 5’ to 3’ direction.

18. Properties of DNA and RNA • They may be informational eg genomic DNA, mRNA. • They may be structural eg rRNA & tRNA. • Retain 5’& 3’ molecular orientation due to nucleotide asymmetry. • They are often single stranded (typically RNA). • They may be extremely long. Movie* • Two polymers (or strands) may become double stranded when certain conditions are met ie they are antiparallel & complementary in nucleotide sequence (typically nuclear DNA). * Terao et al., 2008: Lab on a chip DOI: 10.1039/b803753a

19. 5’Phosphate 3’OH 3’OH 5’Phosphate Duplex DNA is Antiparallel or or 3’ 5’ 3’ 5’ Duplex DNA is NEVER Parallel!

20. Duplex DNA has Complementarity because of Hydrogen Bonds • H bonds are weak (~1/20th of a covalent bond): • Often allows transient contact between molecules (biological signalling systems). • May allow stable contact that can be disrupted and reformed (eg DNA).

21. Hydrogen Bonds • Form between O &/or N with H between them • eg O-H…O, N…H-N or O-H…N. • Are due to electrostatic forces. • H is slightly +ve. • O &/or N are slightly -ve. • Are very weak compared to covalent bonds • May be broken & reform under various chemical or physical conditions.

22. Two representations of duplex DNA showing: • H bonds between bases and, • Covalently bonded Sugar Phosphate backbones. • ~10 basepairs per turn of the helix. • Duplex DNA width = 2nm.

23. Double Stranded (or Duplex) DNA • Is characteristic of genomic DNA. • Consists of two separate nucleic acid polymers (“strands”). • The two strands are Antiparallel wrt 5’& 3’ ends. • They are held together by Hydrogen Bonds between the bases. • H-Bond energies are weak BUT there are many of them which makes the duplex DNA very stable. • Bases are Complementary such that: • A always pairs with T (2 H Bonds). • C always pairs with G (3 H Bonds). • Two strands of complementary antiparallel DNA form a Double Helix eg as found in a chromosome.

24. History of The Double Helix of DNA • The structure of the double helix was found by Rosalind Franklin using X-ray crystallography and correctly interpreted by Watson & Crick in 1953 who also used Chargaff’s rule. • The bases are Hydrophobic and are in the Centre of the helix where complementary bases pair via H-bonding. • The Ribose Sugar and Phosphate groups are on the Outside of the helix where they can H bond to polar solvents like water.

25. Key data that Watson & Crick worked with Xray diffraction pattern of DNA similar to Franklin’s data (above, 1953). Chargaff’s Rule: there is a 1:1 ratio of purines to pyrimidines (because A=T, GºC always). Watson & Crick’s structure for DNA